Merge pull request #81 from neurobagel/maint-44-72

Modified `query_template` in utility.py - Added bg:isSubjectGroup to query_template - Wrapped age, sex, diagnosis, subject group, assessment, and file path with sparql optional pattern
neurobagel · Feb 15, 2023 · 9e1db3c · 9e1db3c
2 parents 2f5e0f3 + 46cfb98
commit 9e1db3c
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Showing 4 changed files with 23 additions and 8 deletions.
diff --git a/app/api/crud.py b/app/api/crud.py
@@ -94,7 +94,7 @@ async def get(
                     dataset=dataset,
                     dataset_name=dataset_name,
                     num_matching_subjects=group["sub_id"].nunique(),
-                    subject_file_paths=list(group["file_path"]),
+                    subject_file_paths=list(group["file_path"].dropna()),
                     image_modals=list(group["image_modal"].unique()),
                 )
             )

diff --git a/app/api/utility.py b/app/api/utility.py
@@ -120,22 +120,35 @@ def create_query(
     SELECT ?dataset ?dataset_name ?sub_id ?file_path ?image_modal
     WHERE {{
     SELECT DISTINCT ?dataset ?dataset_name ?subject ?sub_id ?age ?sex
-    ?diagnosis ?num_sessions ?assessment ?image_modal ?file_path
+    ?diagnosis ?subject_group ?num_sessions ?assessment ?image_modal ?file_path
     WHERE {{
     ?dataset a bg:Dataset;
              bg:label ?dataset_name;
              bg:hasSamples ?subject.
 
     ?subject a bg:Subject;
             bg:label ?sub_id;
-            bg:age ?age;
-            bg:sex ?sex;
-            bg:diagnosis ?diagnosis;
             bg:hasSession ?session;
-            bg:assessment ?assessment;
             bg:hasSession/bg:hasAcquisition/bg:hasContrastType ?image_modal.
 
-    ?session bg:filePath ?file_path.
+    OPTIONAL {{
+        ?session bg:filePath ?file_path.
+    }}
+    OPTIONAL {{
+        ?subject bg:age ?age.
+    }}
+    OPTIONAL {{
+        ?subject bg:sex ?sex.
+    }}
+    OPTIONAL {{
+        ?subject bg:diagnosis ?diagnosis.
+    }}
+    OPTIONAL {{
+        ?subject bg:isSubjectGroup ?subject_group.
+    }}
+    OPTIONAL {{
+        ?subject bg:assessment ?assessment.
+    }}
 
     {{
     SELECT ?subject (count(distinct ?session) as ?num_sessions)

diff --git a/app/main.py b/app/main.py
@@ -4,10 +4,11 @@
 
 import uvicorn
 from fastapi import FastAPI
+from fastapi.responses import ORJSONResponse
 
 from .api.routers import query
 
-app = FastAPI()
+app = FastAPI(default_response_class=ORJSONResponse)
 
 
 @app.on_event("startup")

diff --git a/requirements.txt b/requirements.txt
@@ -15,6 +15,7 @@ identify==2.5.9
 idna==3.4
 iniconfig==1.1.1
 nodeenv==1.7.0
+orjson==3.8.6
 packaging==21.3
 pandas==1.5.2
 platformdirs==2.5.4